Tubulin proteins are essential building blocks of the microtubules of cells, which in turn form a major part of the cellular cytoskeleton and are involved in important cellular functions including intracellular transport, maintenance of cell shape, chromosome segregation during mitosis, and cell motility. Polymers of alpha and beta tubulin subunit heterodimers form hollow cylindrical filament structures which comprise the microtubules. The dynamic between microtubular polymerization and depolymerization is essential to mitosis.
There exist multiple isoforms of the alpha and beta tubulin proteins, with distinct patterns of expression amongst different types of cells such as brain and hematopoietic cells (Drukman et al. 2002, International Journal of Oncology, 21:621-28.). Additionally, some forms of tubulin exist ubiquitously.
Because of the role microtubules play in mitosis, they are attractive targets for chemotherapeutic intervention for cancer. Drugs affecting microtubule function have primarily targeted the alpha and beta tubulin heterodimers, and have been shown to have various binding sites on the heterodimer (Hadfield et al., 2003, Progress in Cell Cycle Research, 5:309-25). Such sites include colchicine, vinca alkaloid, paclitaxel, and other binding sites.
Drugs targeting tubulin form two main families: microtubule-destabilizers and microtubule-stabilizers. Destabilizing agents include the vinca alkaloids, such as vincristine, vinblastine, and vinorelbine. Their mechanism of action is thought to be through tubulin self-association, causing formation of structures other than the normal hollow cylinders of normal microtubules. Stabilizing agents include taxanes like paclitaxel and docetaxel. Their mechanism of action causes the microtubule to stabilize and prevents it from depolymerizing, disrupting the polymerization/depolymerization equilibrium essential for mitosis.
Despite the existence of tubulin-targeting drugs, cancer cells also have exhibited an ability to overcome their effects, becoming resistant to such chemotherapeutic agents. Examples of resistance mechanisms to tubulin-targeting drugs include increased expression and activity of the drug resistant P-glycoprotein (“P-gp”) pump, altered expression of tubulin subtypes and isoforms, mutations in tubulin proteins including in drug binding sites, and post-translational modifications of tubulin proteins such as acetylation. These resistance mechanisms reveal that there is a need for novel chemotherapeutic agents that target tubulin, yet are less susceptible to chemotherapeutic drug resistance.
The identification of tubulin inhibitors can be attempted using methods such as screening of large numbers of random libraries of natural and/or synthetic compounds. However, this method is inefficient in that it typically results in a small number of positive “hits” and is constrained by logistical factors accompanying large screening processes.
Another method of such identification is structure-based drug design (“SBDD”). SBDD comprises a number of integrated components including structural information (eg. spectroscopic data like X-ray or magnetic resonance information, relating to enzyme structure and/or conformation, protein-ligand interactions, etc.), computer modeling, medicinal chemistry, and biological testing (both in vivo and in vitro). These components, each alone or in combination, are useful for accelerating the drug discovery process, for gaining insight into disease and disease processes, and for providing a more efficient method for identifying drug candidates.
Accordingly, the present invention provides compositions and methods related to a design of candidate tubulin inhibitors and methods of treatment thereof.